Archive for July, 2012

Seventy students were involved in a pattern of smartphone-enabled cheating last month at Stuyvesant High School, New York City officials said Monday, describing an episode that has blemished one of the country’s most prestigious public schools.

The cheating involved several state exams and was uncovered after a cellphone was confiscated from a 16-year-old junior during a citywide language exam on June 18, according to a city Department of Education investigation.

It’s not surprising that some doctors would take drug company cash—even when doing so potentially runs counter to the interests of their patients. But the $760 million figure gives a sense how widespread the problem has become. Throw a few names into the ProPublica database—names of medical doctors you know—and there’s a reasonable chance you’ll discover that one has been suckling from Big Pharma’s teat.

And the Libor scandal. Are we seeing the end of the Mandate of Heaven for this ascendant order? Who knows.

A fewpeople have mentioned to me a couple of newpapers in Science are out on rare variants. They’re summed up in a short review article. I suspect this is going to be a big deal for some time. For humans we are coming to toward the end of the SNP-age and entering into the whole-genome-age. That means that the emphasis on common variation at the genomic level is going to give way somewhat to rarer, more particular, variation. One of the major takeaways is that a lot of this variation is going to be population specific. What I am curious about is the pattern of population specificity. For example, we could query the history of consanguinity in the Middle East, or endogamy in India, by the patterns of rare variants, which should crisply demarcate populations as a function of divergence. If I read this right we may be entering into a golden age of demographic history reconstruction, as rare variants and whole-genome catalogs of a huge number of humans are going to allow us to generate a very fine-grained map of human population diversity. Populations are only the start. Ultimately it might be highly informative to compare siblings, who may carry different mutational loads, but share much of the same genetic background.

I found the figure below particularly interesting. Apparently it confirms the recent bottleneck of the Finns:

I’m primarily science blogger, with an amateur interest in history. But I’m still disturbed that over 10 years after 9/11 elite media still can’t be bothered to be precise and accurate about the affairs of the Muslim world. As a neo-Isolationist when it comes to military adventures I wish that ignorance were tolerable, but the reality is that a substantial minority of the populace and the majority of the elite seems intent on flexing American muscle abroad, come hell or national bankruptcy. Instead of imparting to the populace a genuine structure of facts and concepts which adds value in terms of comprehending things as they are, the media seems to just repackage its preconceptions in more sophisticated garb.

Timbuktu now endures the destruction of many of the city’s ancient monuments and religious sites. The devastation is reminiscent of the Taliban’s 2001 attacks on the towering Buddha statues of Bamiyan, Afghanistan. Four of Timbuktu’s landmarks are included on UNESCO’s list of World Heritage sites, but history and heritage mean nothing to the leadership of Ansar Dine, which has destroyed at least six above-ground mausoleums of religious figures regarded as saints and, on Monday, the door of one of the city’s most sacred mosques.

Timbuktu, a center of Sufi mysticism, apparently represents a broad-minded world view at odds with Ansar Dine’s radical conservatism. When asked this week whether the destruction of these cultural artifacts will continue, a spokesman for the sect told the New York Times: “Of course. What doesn’t correspond to Islam, we are going to correct.”

I’ve been thinking that I should post about what it’s been like being a blogger for 10 years. 1/3 of my recollected life! (I recall fragments of being 3, but continuity of self starts somewhere at the end of my 4th year) Actually, I always assumed I would do this post in 2012 when I joined ScienceBlogs in 2006 and realized I could turn this hobby/sidelight into a source of semi-professional fulfillment. But now that the time is nigh (I started blogging in April 2002, while the original Gene Expression launched in June of 2002) I find myself procrastinating, ironic in light of the fact that blogging is often parodied by some as a form of procrastinating. I will say that whenever I have a “9-5″ (or, in my case more often an 8:30 to 6:30 at minimum) I don’t ever write for the blog during those hours (if a post shows up in that period, it’s a feature called scheduling enabling that miracle, something obviously unknown to those readers who stupidly ask “why are you posting now loser! Shouldn’t you be hittin’ on bangin’ chicks, like I am on Friday nights?”). So blogging is not a way procrastinate for me. It is a way to say what I need to say.

But in any case, something over at MetaFilter has prompted me to perhaps reflect on what blogging has become, at least for me. One Allen Spaulding observes:

So I was going to write a whole thing about how this isn’t actually terrible smart writing and that the whole thing reads like a B- paper in Behavioral Econ 201 at a second tier university, but I’ll let this quote do all the work for me:

Second, people who gain a Ph.D. at least know something of theoretical interest. This applies even to an unemployed history Ph.D.!

This is a weird cottage industry – taking obvious problems and using every available tool incorrectly to get clicks so you can sell more ads for penis creme.

Obviously I’m not going to defend my posts on law school as awesome pieces of writing. On the contrary! Yet I’m always aroused toward some curiosity whenever people criticize the content of these non-science related posts. For example, performed a routine analysis of GSS data, and someone in a forum like MetaFilter (I forget which) dismissed the results as something that a graduate student in political science might write as a paper. Here’s the point I want to emphasize: I did not spend more than 30 minutes on the post which the commenter judges as being a B- paper at a second tier university! Question: what’s the going rate for such papers? I could produce a bunch per day if needed. Similarly, the commenter dismissing my GSS posts as something a political science Ph.D. could easily generate might be curious to know that some of my posts of that genre are written in less than 1 hour while I’m killing time in public transportation tethering to my phone so I have an internet connection. The method is rather easy to replicate:

1) Question

2) Look for data sets to test question

Unfortunately not too many people find this practice congenial, so the niche is left to a few odd bloggers (e.g., Audacious Epigone, the Inductivist). Naturally, sometimes I do put a lot of effort into a post. For example, I remember precisely that this post took me about 6 hours total to write. I ran it through two edits, instead of my customary single instance. Though I have to admit here that my very long posts are really not creations de novo, rather, they’re a stitching together of analytic modules I’ve developed over 10 years, or, have had kicking around in the back of my head. Any novel inferences I might have are never obtained through the process of writing. Rather, they serve as seeds for the writing itself.

It’s really pretty simple. There is not a single market for law schools. The market for each applicant is made up solely of those law schools that will accept them.

No one who can get into Harvard would consider going to Whittier law school, whatever the price. But for someone whose LSAT scores place him in the bottow 40% of test takers, that may be the only option. The fact that there are better schools at the same price is completely irrelevant if they won’t accept him.

Similarly, Ohio Northern University has a tuition of ~$35,000 a year. Harvard is ~$38,000. In hindsight the answer is so obvious I’m either stupid or I hadn’t thought deeply about the issue.

End Update

After my last post on law school, one thing is nagging at me: how is it law school tuition isn’t more stretched out in its distribution? Below are the top 10 and bottom 10 in law related job placement, witfh tuition:

One of my major gripes with my friends in ecology is that there is a tendency to look at every problem through the lens of ecological models.Garrett Hardin, who popularized the term “tragedy of the commons” is an exemplar of this. People in ecology often get irritated by the public confusion between it, a positive scientific discipline, and environmentalism, a normative set of beliefs (it doesn’t help when some environmentalist groups have names like “ecology movement”). But the fact is there are deep commonalities in terms of prior assumptions by both ecologists and environmentalists. Despite evolutionary ecology, the reality is that ecologists seem to be characterized by a mindset which posits limits to growth and a finite set of responses to the challenges of scarce resources. That is, the Malthusian paradigm.

I bring this up because despite the similarities between ecology and economics it strikes me that ecologists often have a difficult time admitting that the parameters of the model which they think they have a good grasp of may not always be fixed. Incentives and innovation can shift the dynamics radically. Consider George Monbiot’s about face on “peak oil,” We were wrong on peak oil. There’s enough to fry us all:

…Genetic analysis used to be the most powerful tool for understanding how organisms work, and thus the best skill we could give our students, but its research role has been largely supplanted by molecular methods. Cuts to genetic analysis also threaten the problem-based learning that has been a hallmark of genetics courses. Genetics instructors have all devoted time to developing problems that replicate those arising in real genetics research labs, and a major feature in textbook choice is the quantity and quality of the end-of-chapter problems.

Other cuts will be less traumatic. Our students will probably never need to do a 3-factor cross, except maybe in an outdated genetics laboratory course, nor to analyze phenotypic ratios of progeny, once “one of the pillars of genetics”…There’s also little justification for retaining haploid genetics, fungal genetics, tetrad analysis, and classical somatic-cell genetics in an introductory genetics course. Classical bacterial genetics (conjugation, transduction, transformation) should go too—I’m a bacterial geneticist, so trust me on this one.

I don’t know the answer to the question posted in title above, and I’m moderately skeptical that he has. But I wanted to give him full credit in the public record if researchers confirm his findings in the next few years. You can read the full post at his weblog, but basically he found that a West Asian modal element in a north British (Orkney) and Lithuanian individual seems to be negatively correlated with a Northwest European modal element and positively correlated with Near Eastern and South Asian components on a genomic level across different models in ADMIXTURE (e.g., does “South Asian” at K = 5 tend to match “West Asian” at K = 8).

A few days ago I stumbled upon a really interesting post. And I’m wondering if my readers are at all familiar with the phenomenon outlined here (it was a total surprise to me), The myth of “they weren’t ever taught….”:

Stage One: I will describe this stage for algebra I teachers, but plug in reading, geometry, writing, science, any subject you choose, with the relevant details. This stage begins when teachers realize that easily half the class adds the numerators and denominators when adding fractions, doesn’t see the difference between 3-5 and 5-3, counts on fingers to add 8 and 6, and looks blank when asked what 7 times 3 is.

Ah, they think. The kids weren’t ever taught fractions and basic math facts! What the hell are these other teachers doing, then, taking a salary for showing the kids movies and playing Math Bingo? Insanity on the public penny. But hey, helping these kids, teaching them properly, is the reason they became teachers in the first place. So they push their schedule back, what, two weeks? Three? And go through fraction operations, reciprocals, negative numbers, the meaning of subtraction, a few properties of equality, and just wallow in the glories of basic arithmetic. Some use manipulatives, others use drills and games to increase engagement, but whatever the method, they’re basking in the glow of knowledge that they are Closing the Gap, that their kids are finally getting the attention that privileged suburban students get by virtue of their summer enrichment and more expensive teachers.

At first, it seems to work. The kids beam and say, “You explain it so much better than my last teacher did!” and the quizzes seem to show real progress. Phew! Now it’s possible to get on to teaching algebra, rather than the material the kids just hadn’t been taught.

But then, a few weeks later, the kids go back to ignoring the difference between 3-5 and 5-3. Furthermore, despite hours of explanation and practice, half the class seems to do no better than toss a coin to make the call on positive or negative slopes. Many students who demonstrated mastery of distributing multiplication over addition are now making a complete hash of the process in multi-step equations. And many students are still counting on their fingers.

I’ve been aware of the whole “law school scam” genre for years. The basic issue is pretty straightforward: all the problems of higher education with easy loans and inflated tuition for credentialing are manifest writ large in law schools. Here are some plausible numbers, Law Grads Face Brutal Job Market:

The numbers suggest the job market for law grads is worse than previously thought. Nationwide, only 55% of the class of 2011 had full-time, long-term jobs that required a law degree nine months after graduation. The ABA defines “long-term” jobs as those that don’t have a term of less than one year.

Read the whole article, and you see how law school deans try to present weasel explanations for the damning statistics. There’s also a nice interactive graphic. Whittier College of Law has a 40% unemployment rate for the class of 2011. The bar passage rate is 66%, and the tuition is $38,000. In contrast, Columbia 2011 grads have an unemployment rate of less than 1%, with a tuition of $51,000. Obviously the inputs matter here. Columbia professors aren’t that much better than Whittier professors. Rather, Whittier is probably taking $38,000 a year from individuals who are marginal lawyer material. They’re selling people a dream.

The books you have listed are good ones, by fine people. But may I immodestly suggest a book of mine? If you want to work your way through the theory of theoretical population genetics, I have set of notes for my Genome 562 course, a textbook. It is a freely-downloadable PDF (start with my website by clicking on my name in this comment). It’s not for everyone but I think those interested in knowing how the theory actually works in more detail will benefit from it. As it’s free, I have no monetary interest in calling your attention to it, just pure ego. (And if you want a one-locus population genetics simulation program, try PopG at my lab’s website too — Google “Felsenstein PopG”).

But there is another component present in modern Europe, the West_Asian which is conspicuous in its absence in all the ancient samples so far. This component reaches its highest occurrence in the highlands of West Asia, from Anatolia and the Caucasus all the way to the Indian subcontinent. It is well represented in modern Europeans, reaching its minima in the Iberian peninsula….

Thanks to the public release of genetic data Dienekes has developed his theories in part out of his own analyses of said data. Though I’ve run fewer analyses, with smaller data sets, some of the same patterns jump out at me. In particular, there is a component which is modal in northern West Asia (e.g., the trans-Caucasian region) which seems to drop mysteriously between the French generally and French Basques, and the Basque vs. non-Basque Spanish samples. There are also similar, though not necessarily easy to map across the two regions, disjunctions in South Asia between geographically close Indian groups.

Some people might argue that John Gillespie’s Population Genetics: A Concise Guide (Kindle edition) is a touch too abstruse and cryptic for the introductory reader. It’s short, and the mathematics isn’t challenging, but because of its concision the author can sometimes unleash upon your nearly cryptic formalism, perhaps defeating the purpose of a soft introduction in the first place. To get the most out of this book you probably ironically have to have a more thorough textbook on hand to clear up those particular points which you find confusing. But to get the general logic of population genetics and establish familiarity this seems to be the right entry point (assuming you’re not to terrified by algebra).

Of course most readers of this weblog are focused more particularly on the topic of evolution, and evolutionary genetics. Evolutionary Genetics by the late great John Maynard Smith is a rather good full-spectrum introduction into this topic. It covers many of the topics in the Gillespie book, though less mathematically intensively. But this is not not just a population genetics books, and expands into other topics of relevance to evolutionary genetics (e.g., of course phylogenetics gets a big shout out). And Smith has richer empirical examples too. This is probably a less intimidating book than Population Genetics, but I’d recommend you hit it second because it will make much more sense if you’ve got some of the foundations undernearth you.

Some of you though might be a little on the unbalanced side. I actually “learned” population genetics (if it can be said I know population genetics, I’d more honestly state I’d familiar with population genetics) through Principles of Population Genetics, the “Hartl & Clark” book. This is not really an introductory book, but I think in some ways it’s more comprehensible than Population Genetics, because it doesn’t need to be concise. Sometimes formal methods in pop gen only make sense with lots of empirical examples and worked out problems, and this is a book which has the scope in terms of space for that. There’s really no big downside I can give for getting this book. I’ve got he 2nd, 3rd, and 4th editions, mostly because I couldn’t find an affordable copy of the 3rd in the early 2000s, while the 4th came out literally right after I purchased the 3rd!

This clip with Dan Ariely telling off a dentist who tried to sell him on a more expensive item is classic. Would that we all behaved in such a manner, no? The problem when you interact with a particular set of professionals, in particular in healthcare, the information asymmetry is such that it is very difficult for you to make an informed choice as a consumer. I’ve had an experience very similar to Ariely with dentists.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!